Limit of gui nodes

No need for a native extension if all you want is to change a few pixels (as I imagine is all you need for a led)

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To answer your question regarding texture size, you should use texture large enough so it can keep your entire led matrix without being scaled when rendered. You should scale the actual led graphics when rendering it instead.
If the 2D texture is scaled when rendering, you will either get a jagged or blurry result (depending on your sampling mode). I’m under the impression you’re looking for a 1:1 result of what you rendered given you won’t use texturing for your leds.
Also, some mobile hardware accepts only square power of two size textures, so if you intend this to be your final production solution, you’re best off creating a square texture with the size being the max size of width or height of the matrix.

While rendering to a texture might seem like a quick solution, it quickly gets complicated give different resolutions and even worse if you eventually decide to use textures for the leds.

My personal preferred solution is what Mattias Hedberg suggested above. Use the z-component of the sprites for coloring. That’s a quick solution and it won’t break batching.

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